RSRC1

arginine and serine rich coiled-coil 1

Basic information

Region (hg38): 3:158105855-158545730

Links

ENSG00000174891 ∙ NCBI:51319 ∙ OMIM:613352 ∙ HGNC:24152 ∙ Uniprot:Q96IZ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual developmental disorder, autosomal recessive 70 (Moderate), mode of inheritance: AR
• autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
• intellectual developmental disorder, autosomal recessive 70 (Strong), mode of inheritance: AR
• intellectual developmental disorder, autosomal recessive 70 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual development disorder, autosomal recessive 70	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	28640246; 29522154

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RSRC1 gene.

• Inborn_genetic_diseases (41 variants)
• not_provided (13 variants)
• Intellectual_developmental_disorder,_autosomal_recessive_70 (12 variants)
• RSRC1-related_disorder (2 variants)
• Autism (1 variants)
• Schizophrenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RSRC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001271838.2. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			47	1	1	49
nonsense	2	2				4
start loss	1					1
frameshift	1	1				2
splice donor/acceptor (+/-2bp)	3	1				4
Total	7	4	47	3	1

Highest pathogenic variant AF is 0.000025671625

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RSRC1	protein_coding	protein_coding	ENST00000295930	9	439876

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000745	0.982	125711	0	29	125740	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0946	176	180	0.980	0.0000108	2124
Missense in Polyphen		36	42.971	0.83777		683
Synonymous	-1.10	66	55.6	1.19	0.00000260	632
Loss of Function	2.12	10	20.3	0.493	0.00000126	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000201	0.000193
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in pre-mRNA splicing. Involved in both constitutive and alternative pre-mRNA splicing. May have a role in the recognition of the 3' splice site during the second step of splicing. {ECO:0000269|PubMed:15798186}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.280
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.379
• hipred: N
• hipred_score: 0.390
• ghis: 0.663

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rsrc1

Gene ontology

• Biological process: alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;protein phosphorylation;nucleocytoplasmic transport;RNA splicing;response to antibiotic
• Cellular component: nucleus;cytoplasm;nuclear speck
• Molecular function: protein binding